footer issue

.Rbuildignore

@@ -87,7 +87,6 @@ test-out.xml
 ^pkgdown$
 .lintr
 inst/extdata/toxEval35_endpoint_summary_DLV.xlsx
-inst/shiny/www/footer.html
 vignettes/basicWorkflow.Rmd
 vignettes/shinyApp.Rmd
 vignettes/sidebar.png

CRAN_reminders.txt

@@ -5,3 +5,4 @@ CRAN submissions:
   3. Remove badge links from readme
     (badges made it in last update, so maybe they are OK)
   4. Remove most extraneous links from readme (especially installation)
+5. Figure out what do to with inst/shiny/www/footer.html

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: toxEval
 Type: Package
 Title: Exploring Biological Relevance of Environmental Chemistry Observations
-Version: 1.3.1
+Version: 1.3.2
 Authors@R: c(person("Laura", "DeCicco", 
                      role = c("aut","cre"),
                      email = "[email protected]",
@@ -61,5 +61,4 @@ VignetteBuilder: knitr
 BuildVignettes: true
 LazyLoad: yes
 RoxygenNote: 7.3.1
-Encoding: UTF-8
 

R/toxEval.R

@@ -10,7 +10,7 @@ ToxCast database: version", dbVersion()), width = 40),
 }
 
 dbVersion <- function() {
-  "3.5"
+  "4.0"
 }
 
 #' Analyze ToxCast data in relation to measured concentrations.
@@ -90,7 +90,7 @@ NULL
 #'
 #' @source \doi{10.23645/epacomptox.6062479.v3}
 #' @export end_point_info
-#' @return data frame with 86 columns. The columns and definitions
+#' @return data frame with 72 columns. The columns and definitions
 #' are discussed in the "ToxCast Assay Annotation Version 1.0 Data User Guide (PDF)" (see source).
 #' The column "Relevance Category" was included for consideration of 
 #' grouping/filtering endpoints based on user goals.
@@ -104,7 +104,12 @@ NULL
 # end_point_info <- end_point_info |>
 #   dplyr::select(-reagent_reagent_name_value_type,
 #          -reagent_reagent_name_value,
-#          -citations_citation)
+#          -citations_citation,
+#          -citations_title,
+#          -citations_author,
+#          -assay_source_desc,
+#          -assay_component_endpoint_desc)
+# save(end_point_info, tox_chemicals, ToxCast_ACC, file = "sysdata.rda", compress = "xz")
 
 #' ToxCast Chemical Information
 #'

inst/CITATION

@@ -9,7 +9,7 @@ bibentry(bibtype = "Manual",
               as.person("Gerald T. Ankley")),
   title = "toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.",
   publisher = "U.S. Geological Survey",
-  version = "1.3.1",
+  version = "1.3.2",
   address="Reston, VA",
   institution = "U.S. Geological Survey",
   year = 2024,

vignettes/basicWorkflow.Rmd

@@ -29,7 +29,7 @@ library(dplyr)
 options(continue=" ")
 options(width=60)
 #Set this to TRUE when creating pkgdown site:
-runTables <- TRUE
+runTables <- FALSE
 knitr::opts_chunk$set(echo = TRUE,
                       warning = FALSE,
                       message = FALSE)