Merge pull request #36 from bedapub/chore/cran-submission

Fixes to prepare for CRAN submission

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^designit\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
@@ -19,3 +21,5 @@
 
 # vignette cache
 ^vignettes/cached/.*\.Rmd$
+# large vignette excluded on CRAN
+^vignettes/plate_scoring_examples.Rmd$

DESCRIPTION

@@ -74,6 +74,6 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 biocViews:

NAMESPACE

@@ -1,24 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%>%")
-export(.data)
 export(BatchContainer)
 export(BatchContainerDimension)
 export(L1_norm)
 export(L2s_norm)
 export(accept_leftmost_improvement)
-export(as_label)
-export(as_name)
 export(assign_from_table)
 export(assign_in_order)
 export(assign_random)
 export(batch_container_from_table)
 export(compile_possible_subgroup_allocation)
 export(complete_random_shuffling)
 export(drop_order)
-export(enquo)
-export(enquos)
-export(expr)
 export(first_score_only)
 export(form_homogeneous_subgroups)
 export(generate_terms)
@@ -38,16 +32,8 @@ export(shuffle_grouped_data)
 export(shuffle_with_constraints)
 export(shuffle_with_subgroup_formation)
 export(sum_scores)
-export(sym)
-export(syms)
 export(worst_score)
+import(R6, except = getNamespaceExports("R6"))
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
-importFrom(rlang,as_label)
-importFrom(rlang,as_name)
-importFrom(rlang,enquo)
-importFrom(rlang,enquos)
-importFrom(rlang,expr)
-importFrom(rlang,sym)
-importFrom(rlang,syms)
 importFrom(stats,na.omit)

R/assignment.R

@@ -72,8 +72,8 @@ assign_in_order <- function(batch_container, samples = NULL) {
 #'
 #' @example man/examples/shuffle_with_constraints.R
 shuffle_with_constraints <- function(src = TRUE, dst = TRUE) {
-  src <- enquo(src)
-  dst <- enquo(dst)
+  src <- rlang::enquo(src)
+  dst <- rlang::enquo(dst)
   function(bc, i) {
     dt <- bc$get_samples(include_id = TRUE, as_tibble = FALSE)
     src_ind <- which(rep_len(TRUE, nrow(dt)) & rlang::eval_tidy(src, dt))

R/batch_container.R

@@ -122,6 +122,7 @@ locations_table_from_dimensions <- function(dimensions, exclude) {
 #' A typical workflow starts with creating a `BatchContainer`. Then
 #' samples can be assigned to locations in that container.
 #'
+#' @rawNamespace import(R6, except = getNamespaceExports("R6"))
 #' @export
 BatchContainer <- R6::R6Class("BatchContainer",
   public = list(

R/designit-package.R

@@ -1,6 +1,10 @@
 #' @keywords internal
 "_PACKAGE"
 
+# Manual imports
+#' @importFrom rlang .data
+NULL
+
 # The following block is used by usethis to automatically manage
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start

R/randomization.R

@@ -96,10 +96,10 @@ getScore <- function(layout, balance, sc_groups, sc_tests,
         # get the penalty for each dimension group
         # factor von balace variables
         penalty <- layout %>%
-          dplyr::group_by(!!sym(group)) %>%
+          dplyr::group_by(!!rlang::sym(group)) %>%
           dplyr::summarize_at(.vars = dplyr::vars(balance), testFun)
         score <- penalty %>%
-          dplyr::summarize(score = sum((!!sym(balance))^2, na.rm = TRUE))
+          dplyr::summarize(score = sum((!!rlang::sym(balance))^2, na.rm = TRUE))
         score <- sum(score * bal_weights) # multiply score for each balance factor by its weight and sum
         tscore <- tscore + score
       } else {

R/utils-datatable.R

@@ -1,10 +1,10 @@
-#' This undocumented (?) flag allows us to use `:=`
-#' without getting an error.
-#' @keywords internal
+#' Show that the package is designed to rely on data.table functionality
+#'
+#' See [data.table::let()] and
+#' [`vignette("datatable-importing", "data.table")`](https://cran.r-project.org/web/packages/data.table/vignettes/datatable-importing.html)
+#' section "data.table in Imports but nothing imported".
 #'
-#' @examples
-#' \dontrun{
-#' dt <- data.table::data.table(a = 1, b = 2)
-#' dt[, a := NULL]
-#' }
+#' @keywords internal
+#' @usage NULL
+#' @format NULL
 .datatable.aware <- TRUE

README.Rmd

@@ -36,7 +36,7 @@ devtools::install_github("BEDApub/designit")
 ## Usage
 
 ### R in Pharma presentation
-[![Designit: a flexible engine to generate experiment layouts, R in Pharma presentation](https://img.youtube.com/vi/mvPmSQJVy8o/0.jpg)](http://www.youtube.com/watch?v=mvPmSQJVy8o "Designit: a flexible engine to generate experiment layouts")
+[![Designit: a flexible engine to generate experiment layouts, R in Pharma presentation](https://img.youtube.com/vi/mvPmSQJVy8o/0.jpg)](https://www.youtube.com/watch?v=mvPmSQJVy8o "Designit: a flexible engine to generate experiment layouts")
 
 ### Batch container
 The main class used is `BatchContainer`, which holds the dimensions for sample allocation.

README.md

@@ -25,7 +25,7 @@ devtools::install_github("BEDApub/designit")
 ## Usage
 
 ### R in Pharma presentation
-[![Designit: a flexible engine to generate experiment layouts, R in Pharma presentation](https://img.youtube.com/vi/mvPmSQJVy8o/0.jpg)](http://www.youtube.com/watch?v=mvPmSQJVy8o "Designit: a flexible engine to generate experiment layouts")
+[![Designit: a flexible engine to generate experiment layouts, R in Pharma presentation](https://img.youtube.com/vi/mvPmSQJVy8o/0.jpg)](https://www.youtube.com/watch?v=mvPmSQJVy8o "Designit: a flexible engine to generate experiment layouts")
 
 ### Batch container
 The main class used is `BatchContainer`, which holds the dimensions for

vignettes/plate_layouts.Rmd

@@ -327,7 +327,7 @@ cowplot::plot_grid(
 )
 ```
 
-```{r fig.width=9, fig.height=3}
+```{r fig.width=5.5, fig.height=2}
 bc$scores_table() |>
   ggplot(aes(step, value, color = score)) +
   geom_line() +
@@ -398,7 +398,7 @@ scoring_f <- list(
 bc <- assign_random(bc, subjects)
 ```
 
-```{r, fig.width= 8, fig.height=3}
+```{r, fig.width= 5, fig.height=2}
 cowplot::plot_grid(
   plotlist = list(
     bc$get_samples() %>% ggplot(aes(x = plate, fill = Group)) +
@@ -495,7 +495,7 @@ bc$get_samples() %>%
   unlist()
 ```
 
-```{r, fig.width= 8, fig.height=10}
+```{r, fig.width= 5, fig.height=6.25}
 cowplot::plot_grid(
   plotlist = list(
     plot_plate(bc,
@@ -533,7 +533,7 @@ bc <- optimize_multi_plate_design(bc,
 )
 ```
 
-```{r, fig.width= 8, fig.height=10}
+```{r, fig.width= 5, fig.height=6.25}
 cowplot::plot_grid(
   plotlist = list(
     plot_plate(bc,
@@ -555,7 +555,7 @@ cowplot::plot_grid(
 ```
 
 
-```{r fig.width=6, fig.height=5}
+```{r fig.width=6, fig.height=4}
 bc$scores_table() |>
   ggplot(aes(step, value, color = score)) +
   geom_line() +