Merge pull request #3 from abichat/taxonomy

`step_taxonomy()`

.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

NAMESPACE

@@ -7,27 +7,39 @@ 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)
@@ -37,12 +49,14 @@ export(step_select_background)
 export(step_select_cv)
 export(step_select_kruskal)
 export(step_select_wilcoxon)
+export(step_taxonomy)
 export(var_to_keep)
 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 +73,9 @@ 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 +86,5 @@ importFrom(stats,sd)
 importFrom(stats,wilcox.test)
 importFrom(tibble,enframe)
 importFrom(tibble,tibble)
+importFrom(tidyr,expand_grid)
 importFrom(tidyr,unnest_longer)

NEWS.md

@@ -1,5 +1,7 @@
 # scimo 0.0.1.9000
 
+* New function `step_taxonomy()`.
+
 * Replace superseded `juice()` with `bake(new_data = NULL)` to align with current practices (#1).
 
 

R/aggregate_hclust.R

@@ -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

@@ -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 +22,12 @@ 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

@@ -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

@@ -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

@@ -187,3 +187,9 @@ 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

@@ -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

@@ -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")
+}