follow CRAN directions to include system package data

DESCRIPTION

@@ -63,8 +63,6 @@ Suggests:
     tidyselect,
     vdiffr,
     vol2birdR
-Remotes: 
-    github::adokter/vol2birdR@cran_upload
 LazyData: true
 Encoding: UTF-8
 VignetteBuilder: knitr

NAMESPACE

@@ -76,8 +76,6 @@ S3method(rcs,vpts)
 S3method(sd_vvp_threshold,list)
 S3method(sd_vvp_threshold,vp)
 S3method(sd_vvp_threshold,vpts)
-S3method(select,pvol)
-S3method(select,scan)
 S3method(summary,param)
 S3method(summary,ppi)
 S3method(summary,pvol)
@@ -147,14 +145,8 @@ export(select_vpfiles)
 export(sunrise)
 export(sunset)
 export(update_docker)
-export(validate_vpts)
 export(vol2bird_version)
 export(write_pvolfile)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
-importFrom(dplyr,select)
-importFrom(glue,glue)
 importFrom(methods,as)
-importFrom(readr,read_csv)
-importFrom(stats,na.omit)
-importFrom(stringr,str_detect)

R/as.vpts.R

@@ -2,7 +2,6 @@
 #'
 #' @param data a dataframe created from a VPTS CSV file
 #' @returns a bioRad vpts object
-#' @importFrom glue glue
 #' @examples
 #' # locate example file in VPTS CSV format:
 #' df <- read.csv(system.file("extdata", "example_vpts.csv", package = "bioRad"))

R/hooks.R

@@ -2,10 +2,6 @@
   register_all_s3_methods() # dynamically registers non-imported pkgs (tidyverse) # nocov
 }
 
-.onLoad <- function(libname, pkgname) {
-  data("vpts_schema", package=pkgname, envir=parent.env(environment()))
-}
-
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage(paste("Welcome to", pkgname, "version", utils::packageVersion(pkgname)))
   if (rlang::is_installed("vol2birdR")) {

R/select.R

@@ -1,5 +1,5 @@
 # generalizations for the dplyr verb `select` to `scan` and `pvol` objects
-#' @exportS3Method
+#' @keywords internal
 select.scan <- function(.data, ...) {
   if (!requireNamespace("dplyr", quietly = TRUE)) {
     stop("package dplyr required, please install it first") # nocov
@@ -16,7 +16,7 @@ select.scan <- function(.data, ...) {
   .data
 }
 
-#' @exportS3Method
+#' @keywords internal
 select.pvol <- function(.data, ...) {
   .data$scans <- lapply(.data$scans, select.scan, ...)
   .data

R/validate_vpts.R

@@ -19,19 +19,16 @@ validate_datetime_format <- function(data, format) {
 #' Validate dataframe against VPTS schema
 #'
 #' @param df The dataframe to validate.
-#'
+#' @noRd
 #' @return Invisibly returns a list with validation results including messages for any issues found.
 #' @keywords internal
-#' @examples
-#' my_vpts <- as.data.frame(example_vpts)
-#' validate_vpts(my_vpts)
 validate_vpts <- function(df) {
-    schema <- vpts_schema
+    schema <- bioRad::vpts_schema
     required_fields <- schema$fields$name[schema$fields$constraints.required ==
         TRUE]
     all_fields <- schema$fields$name
     df_fields <- names(df)
-    
+
     # Check for missing required fields
     missing_required <- setdiff(required_fields, df_fields)
     if (length(missing_required) > 0) {