Fixing all data masking notes

NAMESPACE

@@ -91,4 +91,5 @@ importFrom(utils,head)
 importFrom(utils,read.csv)
 importFrom(utils,read.delim)
 importFrom(utils,setTxtProgressBar)
+importFrom(utils,tail)
 importFrom(utils,txtProgressBar)

R/eml.R

@@ -345,7 +345,7 @@ reorder_pids <- function(pid_list, doc){
 #' doc$dataset$project <- proj
 #'
 #' EML::eml_validate(doc)
-#'
+#' @importFrom utils tail
 eml_nsf_to_project <- function(awards, eml_version = "2.2"){
 
   stopifnot(is.character(awards))

R/inventory.R

@@ -270,6 +270,7 @@ inv_load_identifiers <- function(inventory, paths) {
 #' @return (data.frame) An inventory.
 #'
 #' @noRd
+#' @importFrom rlang .data
 inv_add_extra_columns <- function(inventory) {
   stopifnot(is(inventory, "data.frame"), "file" %in% names(inventory))
 
@@ -348,8 +349,8 @@ inv_add_extra_columns <- function(inventory) {
 
   # Calculate statistics related to packages
   cat("Adding 'package_nfiles', 'package_size_mb', and 'package_has_archives' columns.\n")
-  inventory <- dplyr::group_by(inventory, package)
-  inventory <- dplyr::mutate(inventory, package_nfiles = length(package))
+  inventory <- dplyr::group_by(inventory, .data$package)
+  inventory <- dplyr::mutate(inventory, package_nfiles = length(.data$package))
 
   as.data.frame(inventory)
 }

R/marking.R

@@ -35,6 +35,7 @@
 #' @return (data.frame) An inventory.
 #'
 #' @noRd
+#' @importFrom rlang .data
 theme_packages <- function(inventory, nfiles_cutoff=100) {
   stopifnot(is.data.frame(inventory),
             "package_nfiles" %in% names(inventory))
@@ -59,9 +60,9 @@ theme_packages <- function(inventory, nfiles_cutoff=100) {
   inventory$theme[grep("v_\\d\\.", inventory$file)] <- "has-versions"
 
   # There should be no un-themed packages once we're done
-  theme_stats <- dplyr::group_by(inventory, theme)
-  theme_stats <- dplyr::filter(theme_stats, is_metadata == TRUE)
-  theme_stats <- dplyr::summarize(theme_stats, npkgs = length(filename))
+  theme_stats <- dplyr::group_by(inventory, .data$theme)
+  theme_stats <- dplyr::filter(theme_stats, .data$is_metadata == TRUE)
+  theme_stats <- dplyr::summarize(theme_stats, npkgs = length(.data$filename))
 
   cat("Theme summary (by package):\n")
 

R/mosaic.R

@@ -8,6 +8,7 @@
 #' @export
 #'
 #' @examples mosaic_annotate_attribute("PS122/2_14-270")
+#' @importFrom rlang .data
 mosaic_annotate_attribute <- function(eventLabel) {
   # get the owl file from github
   mosaic <- read_ontology("mosaic")
@@ -31,7 +32,7 @@ mosaic_annotate_attribute <- function(eventLabel) {
   stopifnot(eventLabel %in% events$label)
 
   event_device_iri <- events %>%
-    dplyr::filter(label == eventLabel)
+    dplyr::filter(.data$label == eventLabel)
 
   #construct the annotation
   event_annotation <- list(
@@ -70,6 +71,7 @@ mosaic_annotate_attribute <- function(eventLabel) {
 #'
 #' #multiple campaigns
 #' mosaic_annotate_dataset(c("PS122/2", "PS122/1"))
+#' @importFrom rlang .data
 mosaic_annotate_dataset <- function(campaign) {
   check_ps <-
     purrr::map(campaign, ~ stringr::str_detect(.x, "PS", negate = T))
@@ -95,7 +97,7 @@ mosaic_annotate_dataset <- function(campaign) {
 
   stopifnot(campaign %in% df_campaign$label)
 
-  campaign_iri <- dplyr::filter(df_campaign, label %in% campaign)
+  campaign_iri <- dplyr::filter(df_campaign, .data$label %in% campaign)
 
   construct_campaign <- function(label, uri) {
     # Campaign
@@ -153,14 +155,15 @@ query_class <-
 #' mosaic_portal_filter("Basis")
 #'
 #' mosaic_portal_filter("Campaign")
+#' @importFrom rlang .data
 mosaic_portal_filter <- function(class) {
 
   #find the class IRI
   mosaic <- read_ontology("mosaic")
 
   concepts <- get_ontology_concepts(mosaic)
 
-  df_uri <- dplyr::filter(concepts, label == class)
+  df_uri <- dplyr::filter(concepts, .data$label == class)
 
   #build the SPARQL query
   query <-
@@ -204,7 +207,7 @@ mosaic_portal_filter <- function(class) {
     relevant <- unique(unlist(result$sem_annotation))
 
     df <- df %>%
-      dplyr::filter(iri %in% relevant)
+      dplyr::filter(.data$iri %in% relevant)
 
   }
 

R/ontology.R

@@ -72,6 +72,7 @@ get_ontology_concepts <- function(ontology){
 #' @export
 #'
 #' @examples eml_ecso_annotation("latitude coordinate")
+#' @importFrom rlang .data
 eml_ecso_annotation <- function(valueLabel){
 
   ecso <- read_ontology("ecso")
@@ -90,7 +91,7 @@ eml_ecso_annotation <- function(valueLabel){
 
   stopifnot(valueLabel %in% df$label)
 
-  annotations <- dplyr::filter(df, label == valueLabel)
+  annotations <- dplyr::filter(df, .data$label == valueLabel)
 
   list(
     propertyURI = list(label = "contains measurements of type",
@@ -151,6 +152,7 @@ eml_adcad_annotation <- function(valueLabel){
 #' @export
 #'
 #' @examples eml_arcrc_key_variable_annotation("age of sea ice")
+#' @importFrom rlang .data
 eml_arcrc_key_variable_annotation <- function(valueLabel) {
 
   arcrc <- read_ontology("ARCRC")
@@ -169,7 +171,7 @@ eml_arcrc_key_variable_annotation <- function(valueLabel) {
 
   stopifnot(valueLabel %in% df$label)
 
-  annotations <- dplyr::filter(df, label == valueLabel)
+  annotations <- dplyr::filter(df, .data$label == valueLabel)
 
   list(
     propertyURI = list(label = "isAbout",
@@ -190,6 +192,7 @@ eml_arcrc_key_variable_annotation <- function(valueLabel) {
 #' @export
 #'
 #' @examples eml_arcrc_essay_annotation("Sea Ice Indicator")
+#' @importFrom rlang .data
 eml_arcrc_essay_annotation <- function(valueLabel) {
 
   arcrc <- read_ontology("ARCRC")
@@ -208,7 +211,7 @@ eml_arcrc_essay_annotation <- function(valueLabel) {
 
   stopifnot(valueLabel %in% df$label)
 
-  annotations <- dplyr::filter(df, label == valueLabel)
+  annotations <- dplyr::filter(df, .data$label == valueLabel)
 
   list(
     propertyURI = list(label = "influenced",