Merge pull request #4 from abichat/dev

v0.0.2

.github/workflows/R-CMD-check-prdev.yaml

@@ -23,7 +23,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            yatah
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/R-CMD-check.yaml

@@ -41,7 +41,9 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            yatah
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -32,7 +32,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::.
+          extra-packages: |
+            any::pkgdown
+            local::.
+            yatah
           needs: website
 
       - name: Build site

.gitignore

@@ -6,3 +6,4 @@
 .quarto
 inst/doc
 docs
+pkgdown

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scimo
 Title: Extra Recipes Steps for Dealing with Omics Data
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person("Antoine", "BICHAT", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-6599-7081")),

NAMESPACE

@@ -7,42 +7,54 @@ S3method(bake,step_select_background)
 S3method(bake,step_select_cv)
 S3method(bake,step_select_kruskal)
 S3method(bake,step_select_wilcoxon)
+S3method(bake,step_taxonomy)
 S3method(prep,step_aggregate_hclust)
 S3method(prep,step_aggregate_list)
 S3method(prep,step_rownormalize_tss)
 S3method(prep,step_select_background)
 S3method(prep,step_select_cv)
 S3method(prep,step_select_kruskal)
 S3method(prep,step_select_wilcoxon)
+S3method(prep,step_taxonomy)
 S3method(print,step_aggregate_hclust)
 S3method(print,step_aggregate_list)
 S3method(print,step_rownormalize_tss)
 S3method(print,step_select_background)
 S3method(print,step_select_cv)
 S3method(print,step_select_kruskal)
 S3method(print,step_select_wilcoxon)
+S3method(print,step_taxonomy)
+S3method(required_pkgs,step_aggregate_hclust)
+S3method(required_pkgs,step_aggregate_list)
+S3method(required_pkgs,step_rownormalize_tss)
+S3method(required_pkgs,step_select_background)
+S3method(required_pkgs,step_select_cv)
+S3method(required_pkgs,step_select_kruskal)
+S3method(required_pkgs,step_select_wilcoxon)
+S3method(required_pkgs,step_taxonomy)
 S3method(tidy,step_aggregate_hclust)
 S3method(tidy,step_aggregate_list)
 S3method(tidy,step_rownormalize_tss)
 S3method(tidy,step_select_background)
 S3method(tidy,step_select_cv)
 S3method(tidy,step_select_kruskal)
 S3method(tidy,step_select_wilcoxon)
+S3method(tidy,step_taxonomy)
 export("%>%")
-export(cv)
 export(step_aggregate_hclust)
 export(step_aggregate_list)
 export(step_rownormalize_tss)
 export(step_select_background)
 export(step_select_cv)
 export(step_select_kruskal)
 export(step_select_wilcoxon)
-export(var_to_keep)
+export(step_taxonomy)
 importFrom(dplyr,filter)
 importFrom(dplyr,if_else)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
+importFrom(generics,required_pkgs)
 importFrom(generics,tidy)
 importFrom(magrittr,"%>%")
 importFrom(recipes,add_step)
@@ -59,7 +71,9 @@ importFrom(recipes,step)
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,abort)
+importFrom(rlang,call2)
 importFrom(rlang,enquos)
+importFrom(rlang,eval_tidy)
 importFrom(stats,as.formula)
 importFrom(stats,cutree)
 importFrom(stats,dist)
@@ -70,4 +84,5 @@ importFrom(stats,sd)
 importFrom(stats,wilcox.test)
 importFrom(tibble,enframe)
 importFrom(tibble,tibble)
+importFrom(tidyr,expand_grid)
 importFrom(tidyr,unnest_longer)

NEWS.md

@@ -1,3 +1,10 @@
+# scimo 0.0.2
+
+* New function `step_taxonomy()`.
+
+* Replace superseded `juice()` with `bake(new_data = NULL)` to align with current practices (#1).
+
+
 # scimo 0.0.1
 
 * First release of **scimo**.

R/aggregate_hclust.R

@@ -49,7 +49,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_aggregate_hclust <- function(recipe, ..., role = "predictor",
                                   trained = FALSE,
                                   n_clusters,
@@ -200,3 +200,10 @@ tidy.step_aggregate_hclust <- function(x, ...) {
   res$id <- x$id
   res
 }
+
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_aggregate_hclust <- function(x, ...) {
+  c("scimo")
+}

R/aggregate_list.R

@@ -13,10 +13,10 @@
 #' have been estimated.
 #' @param list_agg Named list of aggregated variables.
 #' @param fun_agg  Aggregation function like `sum` or `mean`.
-#' @param others Behavior for the selected variables in `...` that are not present in
-#' `list_agg`. If `discard` (the default), they are not kept. If `asis`, they
-#' are kept without modification. If `aggregate`, they are aggregated in a
-#' new variable.
+#' @param others Behavior for the selected variables in `...` that are not
+#' present in `list_agg`. If `discard` (the default), they are not kept.
+#' If `asis`, they are kept without modification. If `aggregate`, they are
+#' aggregated in a new variable.
 #' @param name_others If `others` is set to `aggregate`, name of the
 #' aggregated variable. Not used otherwise.
 #' @param res This parameter is only produced after the recipe has been trained.
@@ -53,7 +53,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_aggregate_list <- function(recipe, ..., role = "predictor",
                                 trained = FALSE,
                                 list_agg = NULL,
@@ -87,7 +87,7 @@ step_aggregate_list <- function(recipe, ..., role = "predictor",
 
 #' @importFrom recipes step
 step_aggregate_list_new <- function(terms, role, trained,
-                                    list_agg, fun_agg, others,name_others,
+                                    list_agg, fun_agg, others, name_others,
                                     res, prefix, keep_original_cols,
                                     skip, id) {
 
@@ -224,3 +224,10 @@ tidy.step_aggregate_list <- function(x, ...) {
   res$id <- x$id
   res
 }
+
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_aggregate_list <- function(x, ...) {
+  c("scimo")
+}

R/checks.R

@@ -22,3 +22,13 @@ check_binary <- function(x, name_x = "x") {
 
   invisible(x)
 }
+
+
+check_not_null <- function(x, name_x = "x") {
+  if (is.null(x)) {
+    rlang::abort(paste0("`", name_x,
+                        "` must be specified and can't be `NULL`."))
+  }
+
+  invisible(x)
+}

R/rownormalize_tss.R

@@ -36,7 +36,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_rownormalize_tss <- function(recipe, ..., role = NA, trained = FALSE,
                                     res = NULL, skip = FALSE,
                                     id = rand_id("rownormalize_tss")) {
@@ -135,3 +135,9 @@ tidy.step_rownormalize_tss <- function(x, ...) {
   res
 }
 
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_rownormalize_tss <- function(x, ...) {
+  c("scimo")
+}

R/scimo-package.R

@@ -2,7 +2,7 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom generics tidy
+#' @importFrom generics required_pkgs tidy
 #' @importFrom recipes prep bake
 #' @importFrom tibble tibble
 ## usethis namespace: end

R/select_background.R

@@ -41,7 +41,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_select_background <- function(recipe, ..., role = NA, trained = FALSE,
                                    background_level = NULL,
                                    n_samples = NULL,
@@ -184,3 +184,10 @@ tidy.step_select_background <- function(x, ...) {
   res$id <- x$id
   res
 }
+
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_select_background <- function(x, ...) {
+  c("scimo")
+}

R/select_cv.R

@@ -5,14 +5,15 @@
 #' before the computation proceeds. Default to `TRUE`.
 #'
 #' @return The coefficient of variation of `x`.
-#' @export
 #'
 #' @importFrom stats sd
 #'
 #' @author Antoine Bichat
 #'
+#' @keywords internal
+#'
 #' @examples
-#' cv(1:10)
+#' scimo:::cv(1:10)
 cv <- function(x, na.rm = TRUE) {
   sd(x, na.rm = na.rm) / abs(mean(x, na.rm = na.rm))
 }
@@ -59,7 +60,7 @@ cv <- function(x, na.rm = TRUE) {
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_select_cv <- function(recipe, ..., role = NA, trained = FALSE,
                            n_kept = NULL,
                            prop_kept = NULL,
@@ -187,3 +188,9 @@ tidy.step_select_cv <- function(x, ...) {
   res
 }
 
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_select_cv <- function(x, ...) {
+  c("scimo")
+}

R/select_kruskal.R

@@ -24,7 +24,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_select_kruskal <- function(recipe, ..., role = NA, trained = FALSE,
                                 outcome = NULL,
                                 n_kept = NULL,
@@ -179,3 +179,10 @@ tidy.step_select_kruskal <- function(x, ...) {
   res$id <- x$id
   res
 }
+
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_select_kruskal <- function(x, ...) {
+  c("scimo")
+}

R/select_wilcoxon.R

@@ -43,7 +43,7 @@
 #'   prep()
 #' rec
 #' tidy(rec, 1)
-#' juice(rec)
+#' bake(rec, new_data = NULL)
 step_select_wilcoxon <- function(recipe, ..., role = NA, trained = FALSE,
                                  outcome = NULL,
                                  n_kept = NULL,
@@ -199,3 +199,10 @@ tidy.step_select_wilcoxon <- function(x, ...) {
   res$id <- x$id
   res
 }
+
+
+#' @rdname required_pkgs.scimo
+#' @export
+required_pkgs.step_select_wilcoxon <- function(x, ...) {
+  c("scimo")
+}