quash NOTEs

.Rbuildignore

@@ -25,3 +25,4 @@ revdep
 renv.lock
 ^renv\.lock$
 figure
+.github

NAMESPACE

@@ -64,10 +64,13 @@ export(zap_label)
 export(zap_labelled)
 importFrom(dplyr,"%>%")
 importFrom(forcats,as_factor)
+importFrom(graphics,plot)
 importFrom(haven,zap_label)
 importFrom(labelled,"val_label<-")
 importFrom(labelled,"val_labels<-")
 importFrom(labelled,"var_label<-")
 importFrom(labelled,val_label)
 importFrom(labelled,val_labels)
 importFrom(labelled,var_label)
+importFrom(rlang,.data)
+importFrom(vctrs,vec_data)

NEWS.md

@@ -1,6 +1,7 @@
 # codebook 0.9.5
 ## Changes
 - default to psych for reliability because rosetta/ufs is hard to install
+- no longer depends on archived package userfriendlyscience
 ## Bugfixes
 - compatibility with glue 1.8.0
 

R/codebook.R

@@ -1,3 +1,4 @@
+#' @importFrom rlang .data
 .data <- rlang::.data
 
 no_md <- function() {
@@ -26,6 +27,7 @@ no_md <- function() {
 #' @param metadata_json whether to include machine-readable metadata as JSON-LD (not visible)
 #' @param indent add # to this to make the headings in the components lower-level. defaults to beginning at h2
 #'
+#' @importFrom graphics plot
 #' @export
 #' @examples
 #' # will generate figures in a temporary directory
@@ -327,7 +329,8 @@ codebook_missingness <- function(results, indent = "##") {
 #' data("bfi")
 #' metadata_jsonld(bfi)
 metadata_jsonld <- function(results) {
-  jsonld_metadata <- metadata_list(results)
+  jsonld_metadata <- jsonlite::toJSON(metadata_list(results),
+                                      pretty = TRUE, auto_unbox = TRUE)
   rmdpartials::partial(require_file("inst/_metadata_jsonld.Rmd"),
                        name = "metadata_", render_preview = FALSE)
 }

R/codebook_table.R

@@ -107,6 +107,7 @@ attribute_summary <- function(var) {
 #' because the underlying data can be numeric or character. This skimmers summarises
 #' both and leaves non-pertinent columns missings.
 #'
+#' @importFrom vctrs vec_data
 #' @param column the column to skim
 #'
 #' @exportS3Method skimr::get_skimmers haven_labelled

R/detect_scales.R

@@ -13,8 +13,8 @@
 #' @export
 #'
 #' @examples
-#' bfi <- data.frame(matrix(data = rnorm(500), ncol = 5))
-#' names(bfi) <- c("bfi_e1", "bfi_e2R", "bfi_e3", "bfi_n1", "bfi_n2")
+#' bfi <- data.frame(matrix(data = rnorm(300), ncol = 3))
+#' names(bfi) <- c("bfi_e1", "bfi_e2R", "bfi_e3")
 #' bfi$bfi_e <- rowMeans(bfi[, c("bfi_e1", "bfi_e2R", "bfi_e3")])
 #' bfi <- detect_scales(bfi)
 #' bfi$bfi_e

R/reliability.R

@@ -15,11 +15,9 @@
 #'
 #' @export
 #' @examples
-#' \dontrun{
 #' data("bfi", package = "codebook")
 #' bfi <- bfi %>% dplyr::select(dplyr::starts_with("BFIK_agree"))
 #' reliabilities <- compute_reliabilities(bfi)
-#' }
 
 compute_reliabilities <- function(results, survey_repetition = "single",
                                   use_psych = TRUE) {
@@ -109,10 +107,9 @@ compute_appropriate_reliability <- function(scale_name, scale_info,
            "rows need to reflect the earlier measurement occasion, so that ",
            "retest statistics can be computed")
     }
-
-    t1_items <- results[!duplicated(results$session),
+    t1_items <- results[!duplicated(results[, id_vars]),
                         scale_item_names, drop = FALSE]
-    t2_items <- results[duplicated(results$session),
+    t2_items <- results[duplicated(results[, id_vars]),
                         scale_item_names, drop = FALSE]
 
     list(
@@ -137,7 +134,7 @@ compute_appropriate_reliability <- function(scale_name, scale_info,
     long_rel <- tidyr::gather(dplyr::select(dplyr::mutate(
       dplyr::group_by(results, .data$session),
       day_number = as.numeric(.data$created - min(.data$created), unit = 'days')
-      ), session, .data$day_number,
+      ), .data$session, .data$day_number,
       !!!scale_item_names ),
       "variable", "value", -"session", -"day_number")
 

cran-comments.md

@@ -1,11 +1,13 @@
 ## Submission
 * Compatibility with glue 1.8.0
 * Reduced dependencies
+  * no longer suggests archived package userfriendlyscience
   * there are still many dependencies, but these are mainly tidyverse packages, so depending on one, there is little additional cost to depend also on others
   * there are other dependencies I hope to be able to remove soon (e.g., vctrs is only used in testing and for one edge case that a bugfix in haven can eliminate)
 * Updated citation to published paper
+* one declared import (graphics) is used only in one of the rmarkdown partials
+  - inst/codebook_scale.Rmd, line 38
 * Unfortunately, I have had to wrap some examples using the codebook function in dontrun, because I haven't yet figured out how to make rmdpartials switch to "interactive" mode when testing/checking. Once I fix this problem in rmdpartials, I will remove dontrun
-* I also had to wrap the example for `compute_reliabilities` in dontrun, because even a minimal example sometimes takes longer than 10s. I considered using donttest instead, but according to what I could find online donttest is also tested & timed.
 
 ## Test environments
 * local OS X install, R 4.4.1

inst/_metadata_jsonld.Rmd

@@ -1,21 +1,20 @@
 ```{r setup,eval=TRUE,echo=FALSE}
 if (exists("testing")) {
-	indent = '#' # ugly hack so _regression_summary can be "spun" (variables included via `r ` have to be available)
+	indent = '#' # ugly hack so _metadata_jsonld.Rmd can be "spun" (variables included via `r ` have to be available)
 	results = data.frame()
-	jsonld_metadata <- list(test = 1)
+	jsonld_metadata <- jsonlite::toJSON(list(test = 1), pretty = TRUE, auto_unbox = TRUE)
 }
-json <- jsonlite::toJSON(jsonld_metadata, pretty = TRUE, auto_unbox = TRUE)
 ```
 
 <script type="application/ld+json">
-`r json`
+`r jsonld_metadata`
 </script>
 
 <details><summary>JSON-LD metadata</summary>
 The following JSON-LD can be found by search engines, if you share this codebook
 publicly on the web.
 
 ```json
-`r json``
+`r jsonld_metadata``
 ```
 </details>