Merge pull request #420 from tlverse/disable-kerasR

Disables use of `kerasR`
tlverse · Sep 28, 2023 · 64806d5 · 64806d5
2 parents fa669c7 + f6146ea
commit 64806d5
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Showing 78 changed files with 34 additions and 218 deletions.
diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
@@ -29,18 +29,18 @@ jobs:
 
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
       - name: Install pandoc
-        uses: r-lib/actions/setup-pandoc@v1
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install tinyTeX
-        uses: r-lib/actions/setup-tinytex@v1
+        uses: r-lib/actions/setup-tinytex@v2
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
@@ -50,8 +50,7 @@ jobs:
 
       - name: Install package dependencies
         run: |
-          install.packages(c("remotes", "rcmdcheck", "covr", "sessioninfo"))
-          if(Sys.info()["sysname"] == "Windows") install.packages("igraph", type = "binary")
+          install.packages(c("remotes", "devtools", "rcmdcheck", "covr", "sessioninfo"))
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -90,6 +90,7 @@ Suggests:
     mgcv,
     hts,
     GA,
+    SIS,
     partykit
 Remotes:
     github::tlverse/origami,
@@ -106,5 +107,5 @@ VignetteBuilder:
     knitr,
     R.rsp
 Roxygen: list(markdown = TRUE, old_usage = TRUE, r6 = FALSE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 RdMacros: Rdpack
diff --git a/NAMESPACE b/NAMESPACE
@@ -7,7 +7,6 @@ export(Lrnr_arima)
 export(Lrnr_bartMachine)
 export(Lrnr_base)
 export(Lrnr_bayesglm)
-export(Lrnr_bilstm)
 export(Lrnr_bound)
 export(Lrnr_caret)
 export(Lrnr_cv)

diff --git a/R/Lrnr_gts.R b/R/Lrnr_gts.R
@@ -61,8 +61,9 @@
 #'
 #' @examples
 #' # Example adapted from hts package manual
-#' # The hierarchical structure looks like 2 child nodes associated with level 1,
+#' # Hierarchical structure looks like 2 child nodes associated with level 1,
 #' # which are followed by 3 and 2 sub-child nodes respectively at level 2.
+#' library(data.table)
 #' library(hts)
 #'
 #' set.seed(3274)

diff --git a/R/Lrnr_multiple_ts.R b/R/Lrnr_multiple_ts.R
@@ -34,7 +34,7 @@
 #' set.seed(123)
 #'
 #' # Simulate simple AR(2) process
-#' data <- matrix(arima.sim(model = list(ar = c(.9, -.2)), n = 200))
+#' data <- matrix(arima.sim(model = list(ar = c(0.9, -0.2)), n = 200))
 #' id <- c(rep("Series_1", 50), rep("Series_2", 50), rep("Series_3", 50), rep("Series_4", 50))
 #' data <- data.frame(data)
 #' data$id <- as.factor(id)
@@ -45,8 +45,6 @@
 #' data$W1 <- rbinom(200, 1, 0.6)
 #' data$W2 <- rbinom(200, 1, 0.2)
 #'
-#' data <- as.data.table(data)
-#'
 #' folds <- origami::make_folds(data,
 #'   t = max(data$time),
 #'   id = data$id,

diff --git a/R/Lrnr_pca.R b/R/Lrnr_pca.R
@@ -94,12 +94,9 @@ Lrnr_pca <- R6Class(
       return(fit_object)
     },
     .predict = function(task = NULL) {
-      # note that n_comp is an argument not defined in stats::prcomp
+      # note that n_comp is not an argument of stats::prcomp
       dim_args <- self$params[names(self$params) == "n_comp"]
-      preds_rotations <-
-        private$.fit_object$rotation[, seq_len(unlist(dim_args))]
-      preds_pca <- as.matrix(task$X) %*% preds_rotations
-      predictions <- preds_pca
+      predictions <- private$.fit_object$x[, seq_len(unlist(dim_args))]
       return(predictions)
     },
     .required_packages = c("stats")

diff --git a/man/Custom_chain.Rd b/man/Custom_chain.Rd
diff --git a/man/Lrnr_HarmonicReg.Rd b/man/Lrnr_HarmonicReg.Rd
diff --git a/man/Lrnr_arima.Rd b/man/Lrnr_arima.Rd
diff --git a/man/Lrnr_bartMachine.Rd b/man/Lrnr_bartMachine.Rd
diff --git a/man/Lrnr_base.Rd b/man/Lrnr_base.Rd
diff --git a/man/Lrnr_bayesglm.Rd b/man/Lrnr_bayesglm.Rd
diff --git a/man/Lrnr_bilstm.Rd b/man/Lrnr_bilstm.Rd
diff --git a/man/Lrnr_caret.Rd b/man/Lrnr_caret.Rd
diff --git a/man/Lrnr_cv.Rd b/man/Lrnr_cv.Rd
diff --git a/man/Lrnr_cv_selector.Rd b/man/Lrnr_cv_selector.Rd
diff --git a/man/Lrnr_dbarts.Rd b/man/Lrnr_dbarts.Rd
diff --git a/man/Lrnr_define_interactions.Rd b/man/Lrnr_define_interactions.Rd
diff --git a/man/Lrnr_density_discretize.Rd b/man/Lrnr_density_discretize.Rd
diff --git a/man/Lrnr_density_hse.Rd b/man/Lrnr_density_hse.Rd
diff --git a/man/Lrnr_density_semiparametric.Rd b/man/Lrnr_density_semiparametric.Rd
diff --git a/man/Lrnr_earth.Rd b/man/Lrnr_earth.Rd
diff --git a/man/Lrnr_expSmooth.Rd b/man/Lrnr_expSmooth.Rd
diff --git a/man/Lrnr_ga.Rd b/man/Lrnr_ga.Rd
diff --git a/man/Lrnr_gam.Rd b/man/Lrnr_gam.Rd
diff --git a/man/Lrnr_gbm.Rd b/man/Lrnr_gbm.Rd
diff --git a/man/Lrnr_glm.Rd b/man/Lrnr_glm.Rd
diff --git a/man/Lrnr_glm_fast.Rd b/man/Lrnr_glm_fast.Rd
diff --git a/man/Lrnr_glm_semiparametric.Rd b/man/Lrnr_glm_semiparametric.Rd