Cran update

.Rbuildignore

@@ -14,3 +14,5 @@
 ^docs$
 ^pkgdown$
 ^CRAN-SUBMISSION$
+^revdep$
+^vignettes/articles$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: GeoTox
 Title: Spatiotemporal Mixture Risk Assessment
-Version: 0.2.0.9002
+Version: 0.3.0
 Authors@R: c(
     person("Skylar", "Marvel", , "skylar.marvel@nih.gov", role = c("aut"),
            comment = c(ORCID = "0000-0002-2971-9743")),
@@ -49,5 +49,6 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 BugReports: https://github.com/NIEHS/GeoTox/issues
+Config/Needs/website: rmarkdown

NEWS.md

@@ -1,10 +1,12 @@
-# GeoTox (development version)
+# GeoTox 0.3.0
 
-* Fixed a bug that affected sensitivity analysis. The column order of C_ss
-values used for sensitivity analysis is now explicitly ordered similar to other
-functions.
+* `compute_sensitivity()` and the wrapper `sensitivity_analysis()` now use fixed
+Css data with column orders explicitly set to match other functions. The column
+orders are now enforced in the underlying functions `get_fixed_age()`,
+`get_fixed_obesity()`, and `get_fixed_params()`.
 
-* Added set_population() function.
+* Added `set_population()`, which allows for age and/or obesity status to be set
+directly and not require simulation.
 
 * The simulate\_\* functions can now handle population sizes that vary
 across regions.

R/GeoTox.R

@@ -1,41 +1,45 @@
 #' GeoTox S3 object
-#' 
+#'
 #' @description
 #' 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
+#' # See the vignette for a full example:
+#' #   vignette("introduction", package = "geotox")
+#'
+#' \dontrun{
 #' # Use a subset of the package data for demonstration purposes
 #' set.seed(2357)
 #' n <- 10 # Population size
-#' m <- 5 # Number of regions
+#' m <- 2 # Number of regions
 #' idx <- if (m < 100) sample(1:100, m) else 1:100
-#' 
-#' geoTox <- GeoTox() |> 
+#'
+#' geoTox <- GeoTox() |>
 #'   # Set region and group boundaries (for plotting)
 #'   set_boundaries(region = geo_tox_data$boundaries$county,
-#'                  group  = geo_tox_data$boundaries$state) |> 
+#'                  group  = geo_tox_data$boundaries$state) |>
 #'   # Simulate populations for each region
 #'   simulate_population(age           = split(geo_tox_data$age, ~FIPS)[idx],
 #'                       obesity       = geo_tox_data$obesity[idx, ],
 #'                       exposure      = split(geo_tox_data$exposure, ~FIPS)[idx],
 #'                       simulated_css = geo_tox_data$simulated_css,
-#'                       n             = n) |> 
+#'                       n             = n) |>
 #'   # Estimated Hill parameters
 #'   set_hill_params(geo_tox_data$dose_response |>
-#'                     fit_hill(assay = "endp", chem = "casn") |> 
+#'                     fit_hill(assay = "endp", chem = "casn") |>
 #'                     dplyr::filter(!tp.sd.imputed, !logAC50.sd.imputed)) |>
 #'   # Calculate response
 #'   calculate_response() |>
 #'   # Perform sensitivity analysis
 #'   sensitivity_analysis()
-#' 
+#'
 #' # Print GeoTox object
 #' geoTox
-#' 
+#'
 #' # Plot hill fits
 #' plot(geoTox, type = "hill")
 #' # Plot exposure data
@@ -46,6 +50,7 @@
 #' plot(geoTox,
 #'      type = "sensitivity",
 #'      assay = "TOX21_H2AX_HTRF_CHO_Agonist_ratio")
+#' }
 GeoTox <- function() {
   structure(
     list(
@@ -69,7 +74,7 @@ GeoTox <- function() {
 
 #' @export
 print.GeoTox <- function(x, ...) {
-  
+
   # Get n_assay and n_chem from GeoTox()$hill_params
   if (is.null(x$hill_params)) {
     n_assay <- 0
@@ -86,7 +91,7 @@ print.GeoTox <- function(x, ...) {
       n_chem <- 1
     }
   }
-  
+
   # Categorize different GeoTox() fields
   names_data_vec      <- c("age", "IR", "obesity")
   names_data_mat      <- c("C_ext", "C_ss")
@@ -130,19 +135,19 @@ print.GeoTox <- function(x, ...) {
     }
     data.frame(Name = name, Size = size)
   }
-  
+
   # Get size info for each type of field
   info_data <- dplyr::bind_rows(
     purrr::map(names_data_vec, \(name) get_info_vec(name)),
-    purrr::map(names_data_mat, \(name) get_info_mat(name))) |> 
+    purrr::map(names_data_mat, \(name) get_info_mat(name))) |>
     dplyr::filter(.data$Size != "")
-  
+
   info_computed <- dplyr::bind_rows(
     purrr::map(names_computed_mat,  \(name) get_info_mat(name)),
     purrr::map(names_computed_df,   \(name) get_info_df(name)),
-    purrr::map(names_computed_list, \(name) get_info_list(name))) |> 
+    purrr::map(names_computed_list, \(name) get_info_list(name))) |>
     dplyr::filter(.data$Size != "")
-  
+
   # Get population size from GeoTox()$par$n
   if (is.null(x$par$n)) {
     n_pop <- 0
@@ -151,13 +156,13 @@ print.GeoTox <- function(x, ...) {
   } else {
     n_pop <- paste0("[", paste(range(x$par$n), collapse = ", "), "]")
   }
-  
+
   # Get number of regions from potential data fields
   n_region <- purrr::map_int(c(names_data_vec, names_data_mat,
                                names_computed_mat, names_computed_df),
-                             \(name) length(x[[name]])) |> 
+                             \(name) length(x[[name]])) |>
     max()
-  
+
   # Output info
   cat("GeoTox object\n")
   cat("Assays: ", n_assay, "\n", sep = "")

README.Rmd

@@ -59,7 +59,7 @@ Figure 1 below shows the steps in the source-to-outcome-continuum or GeoTox mode
 
 ## Getting Started
 
-Please refer to the [introduction vignette](https://niehs.github.io/GeoTox/articles/introduction.html) for a detailed description of how to use `GeoTox`.
+Please refer to the [package website](https://niehs.github.io/GeoTox/) for a detailed description of how to use `GeoTox`.
 
 ## Citation 
 

README.md

@@ -24,7 +24,6 @@ modeling. The package, methods, and case-studies are described in
 [Messier, Reif, and Marvel, 2025, Human
 Genomics](https://doi.org/10.1186/s40246-024-00711-8).
 
-
 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
@@ -65,9 +64,8 @@ Overview of the steps in the GeoTox framework</em>
 
 ## Getting Started
 
-Please refer to the [introduction
-vignette](https://niehs.github.io/GeoTox/articles/introduction.html) for
-a detailed description of how to use `GeoTox`.
+Please refer to the [package website](https://niehs.github.io/GeoTox/)
+for a detailed description of how to use `GeoTox`.
 
 ## Citation
 

cran-comments.md

@@ -1,5 +1,7 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 0 notes
 
-* This is a new release.
+## revdepcheck results
+
+There are currently no downstream dependencies for this package