diff --git a/.Rbuildignore b/.Rbuildignore index db5fbf4..11d3d39 100644 --- a/.Rbuildignore +++ b/.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 diff --git a/CRAN_reminders.txt b/CRAN_reminders.txt index 82587ac..d299c89 100644 --- a/CRAN_reminders.txt +++ b/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 \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 350516d..1503753 100644 --- a/DESCRIPTION +++ b/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 = "ldecicco@usgs.gov", @@ -61,5 +61,4 @@ VignetteBuilder: knitr BuildVignettes: true LazyLoad: yes RoxygenNote: 7.3.1 -Encoding: UTF-8 diff --git a/R/sysdata.rda b/R/sysdata.rda index d9e285b..120024e 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/R/toxEval.R b/R/toxEval.R index 9284e8f..e2ca0db 100644 --- a/R/toxEval.R +++ b/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 #' diff --git a/inst/CITATION b/inst/CITATION index b15f03e..eeedf66 100644 --- a/inst/CITATION +++ b/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, diff --git a/man/end_point_info.Rd b/man/end_point_info.Rd index 3305579..b55ae29 100644 --- a/man/end_point_info.Rd +++ b/man/end_point_info.Rd @@ -8,7 +8,7 @@ \doi{10.23645/epacomptox.6062479.v3} } \value{ -data frame with 86 columns. The columns and definitions +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. diff --git a/vignettes/basicWorkflow.Rmd b/vignettes/basicWorkflow.Rmd index 8906219..16a88d2 100644 --- a/vignettes/basicWorkflow.Rmd +++ b/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)